RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 01-Jul-2021 23:56:29 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/2_msa/Q9P2R7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/3_mltree/Q9P2R7 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/2_msa/Q9P2R7_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 401 sites

WARNING: Sequences tr_A0A2R8Q7E9_A0A2R8Q7E9_DANRE_7955 and tr_F1R7X5_F1R7X5_DANRE_7955 are exactly identical!
WARNING: Sequences tr_E3S8U4_E3S8U4_PYRTT_861557 and tr_B2WEE5_B2WEE5_PYRTR_426418 are exactly identical!
WARNING: Sequences tr_E3S8U4_E3S8U4_PYRTT_861557 and tr_A0A2W1HIS3_A0A2W1HIS3_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_A0A0E1RW45_A0A0E1RW45_COCIM_246410 and tr_E9D716_E9D716_COCPS_443226 are exactly identical!
WARNING: Sequences tr_A0A0E1RW45_A0A0E1RW45_COCIM_246410 and tr_A0A0J7B9W6_A0A0J7B9W6_COCIT_404692 are exactly identical!
WARNING: Sequences tr_C0NYR4_C0NYR4_AJECG_447093 and tr_C6H530_C6H530_AJECH_544712 are exactly identical!
WARNING: Sequences tr_C0NYR4_C0NYR4_AJECG_447093 and tr_F0UI92_F0UI92_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A179V441_A0A179V441_BLAGS_559298 and tr_C5GWW3_C5GWW3_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2Q7J7_H2Q7J7_PANTR_9598 and tr_A0A2R9BKF1_A0A2R9BKF1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FJA2_F9FJA2_FUSOF_660025 and tr_A0A0D2Y949_A0A0D2Y949_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FJA2_F9FJA2_FUSOF_660025 and tr_A0A2H3TIX8_A0A2H3TIX8_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FJA2_F9FJA2_FUSOF_660025 and tr_A0A2H3GTZ6_A0A2H3GTZ6_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_J4UFB0_J4UFB0_BEAB2_655819 and tr_A0A0A2V528_A0A0A2V528_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4UFB0_J4UFB0_BEAB2_655819 and tr_A0A166S4R6_A0A166S4R6_9HYPO_1081107 are exactly identical!
WARNING: Sequences tr_J4UFB0_J4UFB0_BEAB2_655819 and tr_A0A2N6P322_A0A2N6P322_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A0A0E0IKJ9_A0A0E0IKJ9_ORYNI_4536 and tr_A2X7C5_A2X7C5_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0IKJ9_A0A0E0IKJ9_ORYNI_4536 and tr_I1P2B6_I1P2B6_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0IKJ9_A0A0E0IKJ9_ORYNI_4536 and tr_A0A0E0CNK4_A0A0E0CNK4_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0IKJ9_A0A0E0IKJ9_ORYNI_4536 and tr_A0A0E0NHX7_A0A0E0NHX7_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0IKJ9_A0A0E0IKJ9_ORYNI_4536 and tr_A0A0D3F7R4_A0A0D3F7R4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0IKJ9_A0A0E0IKJ9_ORYNI_4536 and tr_A0A0D9YV44_A0A0D9YV44_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0IKJ9_A0A0E0IKJ9_ORYNI_4536 and sp_Q6K9N6_SUCB_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2R2D0_A2R2D0_ASPNC_425011 and tr_G3XN76_G3XN76_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2R2D0_A2R2D0_ASPNC_425011 and tr_A0A319AMZ2_A0A319AMZ2_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F9X6W9_F9X6W9_ZYMTI_336722 and tr_A0A1X7RNL3_A0A1X7RNL3_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2Y479_G2Y479_BOTF4_999810 and tr_M7TZJ0_M7TZJ0_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_D4APA6_D4APA6_ARTBC_663331 and tr_A0A059JDM5_A0A059JDM5_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_D4APA6_D4APA6_ARTBC_663331 and tr_A0A178EXD4_A0A178EXD4_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3RUL6_B3RUL6_TRIAD_10228 and tr_A0A369S8V2_A0A369S8V2_9METZ_287889 are exactly identical!
WARNING: Sequences tr_W7MZ25_W7MZ25_GIBM7_334819 and tr_A0A2K0WGI1_A0A2K0WGI1_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_M4F5W4_M4F5W4_BRARP_51351 and tr_A0A078H2E0_A0A078H2E0_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M8B120_M8B120_TRIUA_4572 and tr_A0A1D6B2M0_A0A1D6B2M0_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_S0EAE5_S0EAE5_GIBF5_1279085 and tr_N4UNU3_N4UNU3_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_S0EAE5_S0EAE5_GIBF5_1279085 and tr_X0CG98_X0CG98_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_S0EAE5_S0EAE5_GIBF5_1279085 and tr_A0A365NPI3_A0A365NPI3_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_A0A010S728_A0A010S728_9PEZI_1445577 and tr_A0A1G4BCR9_A0A1G4BCR9_9PEZI_1209926 are exactly identical!
WARNING: Sequences tr_A0A067FB34_A0A067FB34_CITSI_2711 and tr_A0A2H5NJI1_A0A2H5NJI1_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A094E0R8_A0A094E0R8_9PEZI_1420912 and tr_A0A1B8GN26_A0A1B8GN26_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0F8V4A0_A0A0F8V4A0_9EURO_308745 and tr_A0A2T5LVA4_A0A2T5LVA4_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0M9EWV4_A0A0M9EWV4_FUSLA_179993 and tr_I1S299_I1S299_GIBZE_229533 are exactly identical!
WARNING: Sequences tr_A0A0M9EWV4_A0A0M9EWV4_FUSLA_179993 and tr_A0A2T4GZD0_A0A2T4GZD0_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A0A1NP16_A0A0A1NP16_9FUNG_58291 and tr_A0A367K298_A0A367K298_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A091KAY6_A0A091KAY6_EGRGA_188379 and tr_A0A091UWV8_A0A091UWV8_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A101M8L8_A0A101M8L8_9EURO_48697 and tr_A0A1V6NJG3_A0A1V6NJG3_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A1S4D955_A0A1S4D955_TOBAC_4097 and tr_A0A1U7XVX2_A0A1U7XVX2_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3NZ88_A0A1S3NZ88_SALSA_8030 and tr_A0A060YPK0_A0A060YPK0_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1R3R9X2_A0A1R3R9X2_ASPC5_602072 and tr_A0A317V8Y0_A0A317V8Y0_9EURO_1450535 are exactly identical!
WARNING: Sequences tr_A0A319CCJ7_A0A319CCJ7_9EURO_1448315 and tr_A0A2V5I3U8_A0A2V5I3U8_9EURO_1450541 are exactly identical!
WARNING: Sequences tr_A0A319CCJ7_A0A319CCJ7_9EURO_1448315 and tr_A0A2V5IVV7_A0A2V5IVV7_9EURO_1450538 are exactly identical!
WARNING: Sequences tr_A0A319EVW4_A0A319EVW4_9EURO_1448318 and tr_A0A395GRI0_A0A395GRI0_9EURO_1448316 are exactly identical!
WARNING: Duplicate sequences found: 50

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/3_mltree/Q9P2R7.raxml.reduced.phy

Alignment comprises 1 partitions and 401 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 401 / 401
Gaps: 1.12 %
Invariant sites: 3.24 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/3_mltree/Q9P2R7.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 201 / 16080
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -514371.367010] Initial branch length optimization
[00:00:05 -439072.057674] Model parameter optimization (eps = 10.000000)
[00:00:43 -438895.969663] AUTODETECT spr round 1 (radius: 5)
[00:03:23 -304261.147747] AUTODETECT spr round 2 (radius: 10)
[00:06:13 -227823.801447] AUTODETECT spr round 3 (radius: 15)
[00:09:35 -178749.583201] AUTODETECT spr round 4 (radius: 20)
[00:13:08 -159296.359871] AUTODETECT spr round 5 (radius: 25)
[00:17:31 -157161.197747] SPR radius for FAST iterations: 25 (autodetect)
[00:17:31 -157161.197747] Model parameter optimization (eps = 3.000000)
[00:17:48 -157067.409734] FAST spr round 1 (radius: 25)
[00:20:55 -134941.750923] FAST spr round 2 (radius: 25)
[00:23:09 -133922.979331] FAST spr round 3 (radius: 25)
[00:25:02 -133869.060659] FAST spr round 4 (radius: 25)
[00:26:45 -133861.128083] FAST spr round 5 (radius: 25)
[00:28:23 -133858.350456] FAST spr round 6 (radius: 25)
[00:29:59 -133858.350439] Model parameter optimization (eps = 1.000000)
[00:30:11 -133856.079435] SLOW spr round 1 (radius: 5)
[00:32:40 -133825.977447] SLOW spr round 2 (radius: 5)
[00:35:00 -133817.804765] SLOW spr round 3 (radius: 5)
[00:37:16 -133813.964304] SLOW spr round 4 (radius: 5)
[00:39:30 -133812.667834] SLOW spr round 5 (radius: 5)
[00:41:43 -133812.667756] SLOW spr round 6 (radius: 10)
[00:43:57 -133812.667756] SLOW spr round 7 (radius: 15)
[00:47:50 -133812.667756] SLOW spr round 8 (radius: 20)
[00:53:42 -133812.667756] SLOW spr round 9 (radius: 25)
[01:01:15 -133812.667756] Model parameter optimization (eps = 0.100000)

[01:01:23] [worker #0] ML tree search #1, logLikelihood: -133812.352634

[01:01:24 -517875.434961] Initial branch length optimization
[01:01:29 -442255.957887] Model parameter optimization (eps = 10.000000)
[01:02:00 -442075.618040] AUTODETECT spr round 1 (radius: 5)
[01:04:37] [worker #1] ML tree search #2, logLikelihood: -133799.182871
[01:04:41 -309709.955028] AUTODETECT spr round 2 (radius: 10)
[01:07:33 -228175.747155] AUTODETECT spr round 3 (radius: 15)
[01:09:43] [worker #2] ML tree search #3, logLikelihood: -133811.587919
[01:10:52 -188907.833575] AUTODETECT spr round 4 (radius: 20)
[01:14:36 -165132.047312] AUTODETECT spr round 5 (radius: 25)
[01:19:18 -161133.907642] SPR radius for FAST iterations: 25 (autodetect)
[01:19:18 -161133.907642] Model parameter optimization (eps = 3.000000)
[01:19:38 -161063.379948] FAST spr round 1 (radius: 25)
[01:22:43 -135437.478844] FAST spr round 2 (radius: 25)
[01:25:04 -134000.883246] FAST spr round 3 (radius: 25)
[01:27:11 -133929.232328] FAST spr round 4 (radius: 25)
[01:28:56 -133922.801660] FAST spr round 5 (radius: 25)
[01:30:38 -133918.109285] FAST spr round 6 (radius: 25)
[01:32:19 -133916.481159] FAST spr round 7 (radius: 25)
[01:33:58 -133916.481145] Model parameter optimization (eps = 1.000000)
[01:34:14 -133912.368376] SLOW spr round 1 (radius: 5)
[01:36:44 -133860.113318] SLOW spr round 2 (radius: 5)
[01:39:13 -133836.177589] SLOW spr round 3 (radius: 5)
[01:41:36 -133831.246072] SLOW spr round 4 (radius: 5)
[01:43:52 -133828.932146] SLOW spr round 5 (radius: 5)
[01:46:06 -133828.931982] SLOW spr round 6 (radius: 10)
[01:48:31 -133821.872873] SLOW spr round 7 (radius: 5)
[01:51:44 -133813.764017] SLOW spr round 8 (radius: 5)
[01:54:21 -133812.612007] SLOW spr round 9 (radius: 5)
[01:56:45 -133810.200284] SLOW spr round 10 (radius: 5)
[01:59:02 -133810.200274] SLOW spr round 11 (radius: 10)
[02:01:19 -133808.733804] SLOW spr round 12 (radius: 5)
[02:04:20 -133808.658703] SLOW spr round 13 (radius: 10)
[02:06:54 -133808.658703] SLOW spr round 14 (radius: 15)
[02:10:27 -133808.658703] SLOW spr round 15 (radius: 20)
[02:16:25 -133808.658703] SLOW spr round 16 (radius: 25)
[02:17:42] [worker #2] ML tree search #6, logLikelihood: -133798.031661
[02:23:51 -133808.658703] Model parameter optimization (eps = 0.100000)

[02:23:58] [worker #0] ML tree search #4, logLikelihood: -133808.598622

[02:23:58 -516134.643192] Initial branch length optimization
[02:24:03 -438523.887573] Model parameter optimization (eps = 10.000000)
[02:24:43 -438310.388088] AUTODETECT spr round 1 (radius: 5)
[02:27:21 -297368.612993] AUTODETECT spr round 2 (radius: 10)
[02:30:13 -220024.814794] AUTODETECT spr round 3 (radius: 15)
[02:31:42] [worker #1] ML tree search #5, logLikelihood: -133804.959992
[02:33:14 -182932.237741] AUTODETECT spr round 4 (radius: 20)
[02:36:51 -171225.432062] AUTODETECT spr round 5 (radius: 25)
[02:41:36 -162404.272472] SPR radius for FAST iterations: 25 (autodetect)
[02:41:36 -162404.272472] Model parameter optimization (eps = 3.000000)
[02:41:56 -162336.853020] FAST spr round 1 (radius: 25)
[02:44:59 -135272.461426] FAST spr round 2 (radius: 25)
[02:47:16 -134041.236743] FAST spr round 3 (radius: 25)
[02:49:19 -133918.173088] FAST spr round 4 (radius: 25)
[02:51:05 -133900.999491] FAST spr round 5 (radius: 25)
[02:52:46 -133894.778224] FAST spr round 6 (radius: 25)
[02:54:25 -133892.165068] FAST spr round 7 (radius: 25)
[02:56:03 -133892.164882] Model parameter optimization (eps = 1.000000)
[02:56:17 -133888.959986] SLOW spr round 1 (radius: 5)
[02:58:51 -133842.711426] SLOW spr round 2 (radius: 5)
[03:01:27 -133822.497083] SLOW spr round 3 (radius: 5)
[03:03:47 -133820.588008] SLOW spr round 4 (radius: 5)
[03:06:02 -133820.587996] SLOW spr round 5 (radius: 10)
[03:08:20 -133820.587996] SLOW spr round 6 (radius: 15)
[03:12:16 -133820.587996] SLOW spr round 7 (radius: 20)
[03:18:05 -133820.587996] SLOW spr round 8 (radius: 25)
[03:25:42 -133820.587996] Model parameter optimization (eps = 0.100000)

[03:25:53] [worker #0] ML tree search #7, logLikelihood: -133820.455522

[03:25:53 -515988.329663] Initial branch length optimization
[03:25:57 -441167.626866] Model parameter optimization (eps = 10.000000)
[03:26:28 -440997.014305] AUTODETECT spr round 1 (radius: 5)
[03:29:07 -306030.528956] AUTODETECT spr round 2 (radius: 10)
[03:29:10] [worker #1] ML tree search #8, logLikelihood: -133822.327954
[03:32:04 -214981.664034] AUTODETECT spr round 3 (radius: 15)
[03:33:17] [worker #2] ML tree search #9, logLikelihood: -133842.471671
[03:35:09 -173683.368430] AUTODETECT spr round 4 (radius: 20)
[03:39:00 -159753.638537] AUTODETECT spr round 5 (radius: 25)
[03:43:20 -156520.699389] SPR radius for FAST iterations: 25 (autodetect)
[03:43:20 -156520.699389] Model parameter optimization (eps = 3.000000)
[03:43:37 -156423.548245] FAST spr round 1 (radius: 25)
[03:46:38 -135101.879587] FAST spr round 2 (radius: 25)
[03:48:53 -133996.869636] FAST spr round 3 (radius: 25)
[03:50:49 -133894.566042] FAST spr round 4 (radius: 25)
[03:52:38 -133878.150711] FAST spr round 5 (radius: 25)
[03:54:18 -133874.692624] FAST spr round 6 (radius: 25)
[03:55:56 -133874.010416] FAST spr round 7 (radius: 25)
[03:57:32 -133874.010411] Model parameter optimization (eps = 1.000000)
[03:57:44 -133871.396246] SLOW spr round 1 (radius: 5)
[04:00:22 -133831.395916] SLOW spr round 2 (radius: 5)
[04:02:42 -133828.912637] SLOW spr round 3 (radius: 5)
[04:04:57 -133828.912637] SLOW spr round 4 (radius: 10)
[04:07:15 -133826.541200] SLOW spr round 5 (radius: 5)
[04:10:16 -133816.605941] SLOW spr round 6 (radius: 5)
[04:12:49 -133816.605744] SLOW spr round 7 (radius: 10)
[04:15:07 -133816.605662] SLOW spr round 8 (radius: 15)
[04:18:50 -133816.605623] SLOW spr round 9 (radius: 20)
[04:24:56 -133816.605603] SLOW spr round 10 (radius: 25)
[04:32:57 -133816.605592] Model parameter optimization (eps = 0.100000)

[04:33:03] [worker #0] ML tree search #10, logLikelihood: -133816.561525

[04:33:03 -515026.102787] Initial branch length optimization
[04:33:08 -437995.806808] Model parameter optimization (eps = 10.000000)
[04:33:44 -437765.630667] AUTODETECT spr round 1 (radius: 5)
[04:35:42] [worker #1] ML tree search #11, logLikelihood: -133836.720645
[04:36:22 -305955.628584] AUTODETECT spr round 2 (radius: 10)
[04:37:52] [worker #2] ML tree search #12, logLikelihood: -133833.839426
[04:39:11 -218509.327538] AUTODETECT spr round 3 (radius: 15)
[04:42:18 -183094.852806] AUTODETECT spr round 4 (radius: 20)
[04:46:16 -166846.463079] AUTODETECT spr round 5 (radius: 25)
[04:50:31 -159757.960531] SPR radius for FAST iterations: 25 (autodetect)
[04:50:31 -159757.960531] Model parameter optimization (eps = 3.000000)
[04:50:47 -159682.503835] FAST spr round 1 (radius: 25)
[04:53:44 -135979.333834] FAST spr round 2 (radius: 25)
[04:56:01 -134156.806950] FAST spr round 3 (radius: 25)
[04:58:02 -133943.547489] FAST spr round 4 (radius: 25)
[04:59:46 -133917.904589] FAST spr round 5 (radius: 25)
[05:01:27 -133906.791611] FAST spr round 6 (radius: 25)
[05:03:05 -133906.791576] Model parameter optimization (eps = 1.000000)
[05:03:16 -133904.648189] SLOW spr round 1 (radius: 5)
[05:05:48 -133858.758741] SLOW spr round 2 (radius: 5)
[05:08:14 -133841.670957] SLOW spr round 3 (radius: 5)
[05:10:31 -133837.101448] SLOW spr round 4 (radius: 5)
[05:12:47 -133835.872233] SLOW spr round 5 (radius: 5)
[05:15:02 -133835.872229] SLOW spr round 6 (radius: 10)
[05:17:16 -133831.553997] SLOW spr round 7 (radius: 5)
[05:20:19 -133828.181215] SLOW spr round 8 (radius: 5)
[05:22:53 -133827.996463] SLOW spr round 9 (radius: 5)
[05:25:27 -133827.020901] SLOW spr round 10 (radius: 5)
[05:27:56 -133825.760956] SLOW spr round 11 (radius: 5)
[05:30:21 -133825.760915] SLOW spr round 12 (radius: 10)
[05:32:46 -133825.760915] SLOW spr round 13 (radius: 15)
[05:32:54] [worker #2] ML tree search #15, logLikelihood: -133846.108686
[05:36:57 -133825.760915] SLOW spr round 14 (radius: 20)
[05:42:49 -133825.760915] SLOW spr round 15 (radius: 25)
[05:47:24] [worker #1] ML tree search #14, logLikelihood: -133811.256244
[05:50:24 -133825.760915] Model parameter optimization (eps = 0.100000)

[05:50:33] [worker #0] ML tree search #13, logLikelihood: -133825.312551

[05:50:33 -516850.485881] Initial branch length optimization
[05:50:38 -440946.217245] Model parameter optimization (eps = 10.000000)
[05:51:13 -440760.534052] AUTODETECT spr round 1 (radius: 5)
[05:53:52 -300035.329305] AUTODETECT spr round 2 (radius: 10)
[05:56:43 -217731.081382] AUTODETECT spr round 3 (radius: 15)
[05:59:47 -188314.869633] AUTODETECT spr round 4 (radius: 20)
[06:03:27 -172332.545828] AUTODETECT spr round 5 (radius: 25)
[06:07:28 -162867.585016] SPR radius for FAST iterations: 25 (autodetect)
[06:07:28 -162867.585016] Model parameter optimization (eps = 3.000000)
[06:07:43 -162791.164281] FAST spr round 1 (radius: 25)
[06:10:52 -137070.798831] FAST spr round 2 (radius: 25)
[06:13:05 -134184.639176] FAST spr round 3 (radius: 25)
[06:15:00 -133867.919525] FAST spr round 4 (radius: 25)
[06:16:45 -133862.000920] FAST spr round 5 (radius: 25)
[06:18:22 -133860.033944] FAST spr round 6 (radius: 25)
[06:19:57 -133860.033942] Model parameter optimization (eps = 1.000000)
[06:20:08 -133856.064548] SLOW spr round 1 (radius: 5)
[06:22:43 -133817.972684] SLOW spr round 2 (radius: 5)
[06:24:58 -133817.972619] SLOW spr round 3 (radius: 10)
[06:27:15 -133817.620721] SLOW spr round 4 (radius: 5)
[06:30:14 -133814.942893] SLOW spr round 5 (radius: 5)
[06:32:47 -133814.942645] SLOW spr round 6 (radius: 10)
[06:35:07 -133814.773394] SLOW spr round 7 (radius: 5)
[06:38:02 -133811.790475] SLOW spr round 8 (radius: 5)
[06:38:49] [worker #2] ML tree search #18, logLikelihood: -133819.097600
[06:40:34 -133811.560851] SLOW spr round 9 (radius: 5)
[06:42:54 -133809.297957] SLOW spr round 10 (radius: 5)
[06:45:09 -133809.297895] SLOW spr round 11 (radius: 10)
[06:47:24 -133809.297895] SLOW spr round 12 (radius: 15)
[06:51:27 -133809.297895] SLOW spr round 13 (radius: 20)
[06:51:49] [worker #1] ML tree search #17, logLikelihood: -133822.034680
[06:57:18 -133809.297895] SLOW spr round 14 (radius: 25)
[07:04:50 -133809.297895] Model parameter optimization (eps = 0.100000)

[07:04:57] [worker #0] ML tree search #16, logLikelihood: -133809.147432

[07:04:57 -518413.030866] Initial branch length optimization
[07:05:01 -440530.873985] Model parameter optimization (eps = 10.000000)
[07:05:38 -440335.835952] AUTODETECT spr round 1 (radius: 5)
[07:08:23 -310449.866910] AUTODETECT spr round 2 (radius: 10)
[07:11:16 -228477.677393] AUTODETECT spr round 3 (radius: 15)
[07:14:28 -189067.111608] AUTODETECT spr round 4 (radius: 20)
[07:18:22 -168877.162765] AUTODETECT spr round 5 (radius: 25)
[07:22:33 -163842.365679] SPR radius for FAST iterations: 25 (autodetect)
[07:22:33 -163842.365679] Model parameter optimization (eps = 3.000000)
[07:22:50 -163762.995677] FAST spr round 1 (radius: 25)
[07:25:55 -136039.449912] FAST spr round 2 (radius: 25)
[07:28:12 -134103.326853] FAST spr round 3 (radius: 25)
[07:30:07 -133911.266229] FAST spr round 4 (radius: 25)
[07:31:50 -133897.272846] FAST spr round 5 (radius: 25)
[07:33:27 -133892.939872] FAST spr round 6 (radius: 25)
[07:35:06 -133889.665761] FAST spr round 7 (radius: 25)
[07:36:45 -133886.259328] FAST spr round 8 (radius: 25)
[07:38:25 -133886.259259] Model parameter optimization (eps = 1.000000)
[07:38:36 -133884.807936] SLOW spr round 1 (radius: 5)
[07:41:13 -133857.069722] SLOW spr round 2 (radius: 5)
[07:43:33 -133856.177664] SLOW spr round 3 (radius: 5)
[07:45:50 -133856.177608] SLOW spr round 4 (radius: 10)
[07:48:03 -133846.986850] SLOW spr round 5 (radius: 5)
[07:51:00 -133845.908139] SLOW spr round 6 (radius: 5)
[07:53:32 -133845.908048] SLOW spr round 7 (radius: 10)
[07:55:45 -133845.908013] SLOW spr round 8 (radius: 15)
[07:59:28 -133845.907980] SLOW spr round 9 (radius: 20)
[08:00:50] [worker #1] ML tree search #20, logLikelihood: -133840.064655
[08:05:11 -133845.907950] SLOW spr round 10 (radius: 25)
[08:12:47 -133845.907921] Model parameter optimization (eps = 0.100000)

[08:12:52] [worker #0] ML tree search #19, logLikelihood: -133845.888584


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.250758,0.212592) (0.288619,0.431987) (0.258558,1.019303) (0.202065,2.763777) 
   Base frequencies (model): 
M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 
M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 
M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 
M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 
   Substitution rates (model): 
M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 
M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 
M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 
M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 


Final LogLikelihood: -133798.031661

AIC score: 271606.063322 / AICc score: 8315666.063322 / BIC score: 279613.955984
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=401).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/3_mltree/Q9P2R7.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/3_mltree/Q9P2R7.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/3_mltree/Q9P2R7.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9P2R7/3_mltree/Q9P2R7.raxml.log

Analysis started: 01-Jul-2021 23:56:29 / finished: 02-Jul-2021 08:09:22

Elapsed time: 29572.376 seconds

Consumed energy: 2582.425 Wh (= 13 km in an electric car, or 65 km with an e-scooter!)